Dear Daniel,
As I said $AMBERHOME is in my path.
gm.linux-rfml:/usr/local/amber12> echo $PATH
/home/vaibhav/bin/oniomtool:/home/vaibhav/software/vmd_files_exceutables/start_scripts/:/home/vaibhav/bin/oniomtool:/home/vaibhav/software/vmd_files_exceutables/start_scripts/:/home/gm/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/jvm/jre/bin:/usr/local/amber12/exe:/usr/local/amber12/exe
gm.linux-rfml:/usr/local/amber12>
gm.linux-rfml:~> cd $AMBERHOME
gm.linux-rfml:/usr/local/amber12>
On Thu, Jan 31, 2013 at 11:31 AM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> Is $AMBERHOME/bin in your path? If not add it as per the installation
> instructions in the manual.
> try
> echo $PATH
>
>
>
>
> On Thu, Jan 31, 2013 at 2:53 PM, Vaibhav Dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Jason, Daniel and Amber users,
> > The make install and make test command ran perfectly, but strangely I'm
> not
> > able to run any command on the terminal. It gives the following message
> for
> > commands like sander, ptraj, tleap etc. I have checked $AMBERHOME is set
> > correctly. I wonder if some links were not properly created or what?
> Please
> > help me track the problem and let me know if more information is needed
> to
> > understand issue.
> >
> > gm.linux-rfml:/usr/local/amber12> ptraj
> > If 'ptraj' is not a typo you can use command-not-found to lookup the
> > package that contains it, like this:
> > cnf ptraj
> > gm.linux-rfml:/usr/local/amber12>
> >
> >
> >
> > ==============================================================
> >
> > Finished serial test suite for Amber 12 at Thu Jan 31 10:34:39 IST 2013.
> >
> > make[2]: Leaving directory `/usr/local/amber12/test'
> > 478 file comparisons passed
> > 1 file comparisons failed
> > 1 tests experienced errors
> > Test log file saved as
> > /usr/local/amber12/logs/test_amber_serial/2013-01-31_10-14-41.log
> > Test diffs file saved as
> > /usr/local/amber12/logs/test_amber_serial/2013-01-31_10-14-41.diff
> > make[1]: Leaving directory `/usr/local/amber12/test'
> >
> > Summary of AmberTools serial tests:
> >
> > 607 file comparisons passed
> > 3 file comparisons failed
> > 0 tests experienced errors
> > Test log file saved as
> > /usr/local/amber12/logs/test_at_serial/2013-01-31_09-47-13.log
> > Test diffs file saved as
> > /usr/local/amber12/logs/test_at_serial/2013-01-31_09-47-13.diff
> >
> >
> > On Wed, Jan 30, 2013 at 6:58 PM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > On Wed, Jan 30, 2013 at 8:11 AM, Vaibhav Dixit <
> vaibhavadixit.gmail.com
> > > >wrote:
> > >
> > > > Dear Daniel and Jason,
> > > > I realized my mistake of not recognizing the correct patches.
> > > > After I have downloaded the correct patches, it seems that things
> have
> > > > worked fine. As suggested on the site I have run the command
> > > > (./patch_amber.py) twice. At present I'm running the "make install"
> > > > command.
> > > > Regarding the proxy setting I did not really understand the
> discussion
> > as
> > > > I'm not a networking expert.
> > > > But I'm happy that the other way round seems to have worked. (With
> > amber
> > > > there is something new to learn everyday).
> > > > Thanks all for your time and suggestions.
> > > >
> > > > ---------
> > > > linux-rfml:/usr/local/amber12 # ./patch_amber.py --update-tree
> > > > Determining patches to download for AmberTools12
> > > > AmberTools12 is up to date. Nothing to download
> > > >
> > >
> > > Don't forget to add the AmberTools bug fixes to that repository. I'm
> > > skeptical they have all been added already.
> > >
> > > Good luck,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D.
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408, +91-7709129400.
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dr. Daniel J. Sindhikara <http://www.dansindhikara.com/Information.html>
> Ritsumeikan University <http://www.ritsumei.ac.jp/eng/>
> sindhikara.gmail.com <http://www.dansindhikara.com>
> --
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Wed Jan 30 2013 - 22:30:03 PST
